Added automatic sample name replacement

tests/modvcfsamples/test_sample.py

@@ -2,6 +2,7 @@ from modvcfsamples.sample import (
     keep_specific_call_data,
     get_records_from_vcf,
     normalize_gt_to_length,
+    replace_sample_names,
 )
 import os
 
@@ -32,7 +33,7 @@ def test_normalize_gt_to_length_not_empty():
     records, header = get_records_from_vcf(
         os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
     )
-    modified_records, _ = normalize_gt_to_length(records, header, 4)
+    modified_records = normalize_gt_to_length(records, 4)
     assert len(modified_records) > 0
 
 
@@ -40,7 +41,37 @@ def test_normalize_gt_to_length_gt_normalized():
     records, header = get_records_from_vcf(
         os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
     )
-    modified_records, _ = normalize_gt_to_length(records, header, 4)
+    modified_records = normalize_gt_to_length(records, 4)
     for modified_record in modified_records:
         for call in modified_record.calls:
             assert len(call.data["GT"].split("|")) == 4 or "/" in call.data["GT"]
+
+def test_replace_sample_names_record_modified_correctly():
+    records, header = get_records_from_vcf(
+        os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
+    )
+    modified_records, modified_headers = replace_sample_names(records, header, "Gambian", "different")
+    for modified_record in modified_records:
+        call_name_replaced = False
+        for call in modified_record.calls:
+            assert call.sample != "Gambian"
+            if call.sample == "different":
+                call_name_replaced = True
+        assert call_name_replaced
+
+
+def test_replace_sample_names_header_modified_correctly():
+    records, header = get_records_from_vcf(
+        os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
+    )
+    modified_records, modified_headers = replace_sample_names(records, header, "Gambian", "different")
+    replaced_found = False
+    original_found = False
+    for name in modified_headers.samples.names:
+        if name == "Gambian":
+            original_found = True
+
+        if name == "different":
+            replaced_found = True
+    assert replaced_found
+    assert not original_found